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An open-source solution for advanced imaging flow cytometry data analysis using machine learning.
Hennig H, Rees P, Blasi T, et al. An open-source solution for advanced imaging flow cytometry data analysis using machine learning. Methods. 2017;112:201-210. doi:10.1016/j.ymeth.2016.08.018.
Cell Painting, a high-content image-based assay for morphological profiling using multiplexed fluorescent dyes.
Bray M-A, Singh S, Han H, et al. Cell Painting, a high-content image-based assay for morphological profiling using multiplexed fluorescent dyes. Nat Protoc. 2016;11(9):1757-74. doi:10.1038/nprot.2016.105.
High-Throughput Platform for Identifying Molecular Factors Involved in Phenotypic Stabilization of Primary Human Hepatocytes In Vitro.
Shan J, Logan DJ, Root DE, Carpenter AE, Bhatia SN. High-Throughput Platform for Identifying Molecular Factors Involved in Phenotypic Stabilization of Primary Human Hepatocytes In Vitro. J Biomol Screen. 2016;21(9):897-911. doi:10.1177/1087057116660277.
Quantifying co-cultured cell phenotypes in high-throughput using pixel-based classification.
Logan DJ, Shan J, Bhatia SN, Carpenter AE. Quantifying co-cultured cell phenotypes in high-throughput using pixel-based classification. Methods. 2016;96:6-11. doi:10.1016/j.ymeth.2015.12.002.
CellProfiler Analyst: interactive data exploration, analysis and classification of large biological image sets.
Dao D, Fraser AN, Hung J, Ljosa V, Singh S, Carpenter AE. CellProfiler Analyst: interactive data exploration, analysis and classification of large biological image sets. Bioinformatics. 2016. doi:10.1093/bioinformatics/btw390.
An open-source computational tool to automatically quantify immunolabeled retinal ganglion cells.
Dordea AC, Bray M-A, Allen K, et al. An open-source computational tool to automatically quantify immunolabeled retinal ganglion cells. Exp Eye Res. 2016;147:50-6. doi:10.1016/j.exer.2016.04.012.
QSAR-Driven Discovery of Novel Chemical Scaffolds Active against Schistosoma mansoni.
Melo-Filho CC, Dantas RF, Braga RC, et al. QSAR-Driven Discovery of Novel Chemical Scaffolds Active against Schistosoma mansoni. J Chem Inf Model. 2016;56(7):1357-72. doi:10.1021/acs.jcim.6b00055.
CP-CHARM: segmentation-free image classification made accessible.
Uhlmann V, Singh S, Carpenter AE. CP-CHARM: segmentation-free image classification made accessible. BMC Bioinformatics. 2016;17:51. doi:10.1186/s12859-016-0895-y.
A Genome-wide RNAi Screen for Microtubule Bundle Formation and Lysosome Motility Regulation in Drosophila S2 Cells.
Jolly AL, Luan C-H, Dusel BE, et al. A Genome-wide RNAi Screen for Microtubule Bundle Formation and Lysosome Motility Regulation in Drosophila S2 Cells. Cell Rep. 2016;14(3):611-20. doi:10.1016/j.celrep.2015.12.051.
Label-free cell cycle analysis for high-throughput imaging flow cytometry.
Blasi T, Hennig H, Summers HD, et al. Label-free cell cycle analysis for high-throughput imaging flow cytometry. Nat Commun. 2016;7:10256. doi:10.1038/ncomms10256.
CellProfiler Tracer: exploring and validating high-throughput, time-lapse microscopy image data.
Bray M-A, Carpenter AE. CellProfiler Tracer: exploring and validating high-throughput, time-lapse microscopy image data. BMC Bioinformatics. 2015;16:368. doi:10.1186/s12859-015-0759-x.
Using CellProfiler for Automatic Identification and Measurement of Biological Objects in Images.
Bray M-A, Vokes MS, Carpenter AE. Using CellProfiler for Automatic Identification and Measurement of Biological Objects in Images. Curr Protoc Mol Biol. 2015;109:14.17.1-13. doi:10.1002/0471142727.mb1417s109.
CDy6, a photostable probe for long-term real-time visualization of mitosis and proliferating cells.
Jeong Y-M, Duanting Z, Hennig H, et al. CDy6, a photostable probe for long-term real-time visualization of mitosis and proliferating cells. Chem Biol. 2015;22(2):299-307. doi:10.1016/j.chembiol.2014.11.018.
Crowdsourcing the creation of image segmentation algorithms for connectomics.
Arganda-Carreras I, Turaga SC, Berger DR, et al. Crowdsourcing the creation of image segmentation algorithms for connectomics. Front Neuroanat. 2015;9:142. doi:10.3389/fnana.2015.00142.
Morphological Profiles of RNAi-Induced Gene Knockdown Are Highly Reproducible but Dominated by Seed Effects.
Singh S, Wu X, Ljosa V, et al. Morphological Profiles of RNAi-Induced Gene Knockdown Are Highly Reproducible but Dominated by Seed Effects. PLoS One. 2015;10(7):e0131370. doi:10.1371/journal.pone.0131370.
Increased expression of the immune modulatory molecule PD-L1 (CD274) in anaplastic meningioma.
Du Z, Abedalthagafi M, Aizer AA, et al. Increased expression of the immune modulatory molecule PD-L1 (CD274) in anaplastic meningioma. Oncotarget. 2014. Available at: http://www.impactjournals.com/oncotarget/misc/linkedout.php?pii=3082.
Nanoparticle vesicle encoding for imaging and tracking cell populations.
Rees P, Wills JW, M Brown R, et al. Nanoparticle vesicle encoding for imaging and tracking cell populations. Nat Methods. 2014;11(11):1177-81. doi:10.1038/nmeth.3105.
Increasing the Content of High-Content Screening: An Overview.
Singh S, Carpenter AE, Genovesio A. Increasing the Content of High-Content Screening: An Overview. J Biomol Screen. 2014;19(5):640-50. doi:10.1177/1087057114528537.
ZFHX4 interacts with the NuRD core member CHD4 and regulates the glioblastoma tumor-initiating cell state.
Chudnovsky Y, Kim D, Zheng S, et al. ZFHX4 interacts with the NuRD core member CHD4 and regulates the glioblastoma tumor-initiating cell state. Cell Rep. 2014;6(2):313-24. doi:10.1016/j.celrep.2013.12.032.
Identification of host-targeted small molecules that restrict intracellular Mycobacterium tuberculosis growth.
Stanley SA, Barczak AK, Silvis MR, et al. Identification of host-targeted small molecules that restrict intracellular Mycobacterium tuberculosis growth. PLoS Pathog. 2014;10(2):e1003946. doi:10.1371/journal.ppat.1003946.
ProtocolNavigator: emulation-based software for the design, documentation and reproduction biological experiments.
Khan IA, Fraser A, Bray M-A, et al. ProtocolNavigator: emulation-based software for the design, documentation and reproduction biological experiments. Bioinformatics. 2014;30(23):3440-2. doi:10.1093/bioinformatics/btu554.
Pipeline for illumination correction of images for high-throughput microscopy.
Singh S, Bray M-A, Jones TR, Carpenter AE. Pipeline for illumination correction of images for high-throughput microscopy. J Microsc. 2014;256(3):231-6. doi:10.1111/jmi.12178.
High- and low-throughput scoring of fat mass and body fat distribution in C. elegans.
Wählby C, Conery ALee, Bray M-A, et al. High- and low-throughput scoring of fat mass and body fat distribution in C. elegans. Methods. 2014;68(3):492-9. doi:10.1016/j.ymeth.2014.04.017.
High content image analysis identifies novel regulators of synaptogenesis in a high-throughput RNAi screen of primary neurons.
Nieland TJF, Logan DJ, Saulnier J, et al. High content image analysis identifies novel regulators of synaptogenesis in a high-throughput RNAi screen of primary neurons. PLoS One. 2014;9(3):e91744. doi:10.1371/journal.pone.0091744.
A microscale human liver platform that supports the hepatic stages of Plasmodium falciparum and vivax.
March S, Ng S, Velmurugan S, et al. A microscale human liver platform that supports the hepatic stages of Plasmodium falciparum and vivax. Cell Host Microbe. 2013;14(1):104-15. doi:10.1016/j.chom.2013.06.005.
Comparison of methods for image-based profiling of cellular morphological responses to small-molecule treatment.
Ljosa V, Caie PD, Horst RTer, et al. Comparison of methods for image-based profiling of cellular morphological responses to small-molecule treatment. J Biomol Screen. 2013;18(10):1321-9. doi:10.1177/1087057113503553.
Niche-based screening identifies small-molecule inhibitors of leukemia stem cells.
Hartwell KA, Miller PG, Mukherjee S, et al. Niche-based screening identifies small-molecule inhibitors of leukemia stem cells. Nat Chem Biol. 2013;9(12):840-8. doi:10.1038/nchembio.1367.
Identification of small molecules for human hepatocyte expansion and iPS differentiation.
Shan J, Schwartz RE, Ross NT, et al. Identification of small molecules for human hepatocyte expansion and iPS differentiation. Nat Chem Biol. 2013;9(8):514-20. doi:10.1038/nchembio.1270.
Multiplex cytological profiling assay to measure diverse cellular states.
Gustafsdottir SM, Ljosa V, Sokolnicki KL, et al. Multiplex cytological profiling assay to measure diverse cellular states. PLoS One. 2013;8(12):e80999. doi:10.1371/journal.pone.0080999.
Annotated high-throughput microscopy image sets for validation.
Ljosa V, Sokolnicki KL, Carpenter AE. Annotated high-throughput microscopy image sets for validation. Nat Methods. 2012;9(7):637. doi:10.1038/nmeth.2083.
A call for bioimaging software usability.
Carpenter AE, Kamentsky L, Eliceiri KW. A call for bioimaging software usability. Nat Methods. 2012;9(7):666-70. doi:10.1038/nmeth.2073.
Workflow and metrics for image quality control in large-scale high-content screens.
Bray M-A, Fraser AN, Hasaka TP, Carpenter AE. Workflow and metrics for image quality control in large-scale high-content screens. J Biomol Screen. 2012;17(2):266-74. doi:10.1177/1087057111420292.
Identification of regulators of polyploidization presents therapeutic targets for treatment of AMKL.
Wen Q, Goldenson B, Silver SJ, et al. Identification of regulators of polyploidization presents therapeutic targets for treatment of AMKL. Cell. 2012;150(3):575-89. doi:10.1016/j.cell.2012.06.032.
An image analysis toolbox for high-throughput C. elegans assays.
Wählby C, Kamentsky L, Liu ZH, et al. An image analysis toolbox for high-throughput C. elegans assays. Nat Methods. 2012;9(7):714-6. doi:10.1038/nmeth.1984.
A chemical screen probing the relationship between mitochondrial content and cell size.
Kitami T, Logan DJ, Negri J, et al. A chemical screen probing the relationship between mitochondrial content and cell size. PLoS One. 2012;7(3):e33755. doi:10.1371/journal.pone.0033755.
Human tumors instigate granulin-expressing hematopoietic cells that promote malignancy by activating stromal fibroblasts in mice.
Elkabets M, Gifford AM, Scheel C, et al. Human tumors instigate granulin-expressing hematopoietic cells that promote malignancy by activating stromal fibroblasts in mice. J Clin Invest. 2011;121(2):784-99. doi:10.1172/JCI43757.
Visualization of parameter space for image analysis.
A Pretorius J, Bray M-AP, Carpenter AE, Ruddle RA. Visualization of parameter space for image analysis. IEEE Trans Vis Comput Graph. 2011;17(12):2402-11. doi:10.1109/TVCG.2011.253.
Screening cellular feature measurements for image-based assay development.
Logan DJ, Carpenter AE. Screening cellular feature measurements for image-based assay development. J Biomol Screen. 2010;15(7):840-6. doi:10.1177/1087057110370895.
Scoring diverse cellular morphologies in image-based screens with iterative feedback and machine learning.
Jones TR, Carpenter AE, Lamprecht MR, et al. Scoring diverse cellular morphologies in image-based screens with iterative feedback and machine learning. Proc Natl Acad Sci U S A. 2009;106(6):1826-31. doi:10.1073/pnas.0808843106.
Introduction to the quantitative analysis of two-dimensional fluorescence microscopy images for cell-based screening.
Ljosa V, Carpenter AE. Introduction to the quantitative analysis of two-dimensional fluorescence microscopy images for cell-based screening. PLoS Comput Biol. 2009;5(12):e1000603. doi:10.1371/journal.pcbi.1000603.
Ultrasome: efficient aberration caller for copy number studies of ultra-high resolution.
Nilsson B, Johansson M, Al-Shahrour F, Carpenter AE, Ebert BL. Ultrasome: efficient aberration caller for copy number studies of ultra-high resolution. Bioinformatics. 2009;25(8):1078-9. doi:10.1093/bioinformatics/btp091.
Extracting rich information from images.
Carpenter AE. Extracting rich information from images. Methods Mol Biol. 2009;486:193-211. doi:10.1007/978-1-60327-545-3_14.
High-throughput screens for fluorescent dye discovery.
Ljosa V, Carpenter AE. High-throughput screens for fluorescent dye discovery. Trends Biotechnol. 2008;26(10):527-30. doi:10.1016/j.tibtech.2008.06.008.
CellProfiler Analyst: data exploration and analysis software for complex image-based screens.
Jones TR, Kang IHan, Wheeler DB, et al. CellProfiler Analyst: data exploration and analysis software for complex image-based screens. BMC Bioinformatics. 2008;9:482. doi:10.1186/1471-2105-9-482.
Image-based chemical screening.
Carpenter AE. Image-based chemical screening. Nat Chem Biol. 2007;3(8):461-5. doi:10.1038/nchembio.2007.15.